Barry, That issue + this commit: $ git bisect bad 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 is the first bad commit commit 36c166f2bbb44c2987d8fb7385fbe9e2d1cfb0c8 Author: Barry Smith <bsm...@mcs.anl.gov> Date: Sat Apr 10 13:40:10 2021 -0500 makes it actually impossible to ./configure on macOS. Do we really expect all macOS users to know about the variable MACOSX_DEPLOYMENT_TARGET?
Thanks, Pierre $ ./configure =============================================================================== Configuring PETSc to compile on your system =============================================================================== TESTING: checkFortranLibraries from config.compilers(config/BuildSystem/config/compilers.py:921) ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Fortran libraries cannot be used with C as linker ******************************************************************************* Executing: mpicc -o /var/folders/_9/0qn1m4z92wzbhz9434vx39fc0000gn/T/petsc-bhav6feq/config.setCompilers/conftest -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fno-stack-check -Qunused-arguments -fvisibility=hidden -g3 /var/folders/_9/0qn1m4z92wzbhz9434vx39fc0000gn/T/petsc-bhav6feq/config.setCompilers/conftest.o -lc++ -ldl -lc++ -ldl -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib -L/usr/local/Cellar/mpich/3.4.1_1/lib -lmpifort -lmpi -lpmpi -lgfortran -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lgfortran -lquadmath -lm Possible ERROR while running linker: stderr: ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) was built for newer macOS version (11.2) than being linked (11.0) ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built for newer macOS version (11.2) than being linked (11.0) ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built for newer macOS version (11.2) than being linked (11.0) ld: warning: dylib (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built for newer macOS version (11.2) than being linked (11.0) compilers: Cannot compile/link C with mpicc. > On 12 Mar 2021, at 6:16 PM, Barry Smith <bsm...@petsc.dev> wrote: > > > You should be able to edit lib/petsc/conf/rules and add it to the filter > for .cu.PETSc .kokkos.cxx.PETSc .c.PETSc .cxx.PETSc: and .F.PETSc .F90.PETSc: > > I think it is fine to hide this warning; it is impossible for me to > understand anyway :-(. > > Barry > > > > >> On Mar 12, 2021, at 2:44 AM, Pierre Jolivet <pie...@joliv.et >> <mailto:pie...@joliv.et>> wrote: >> >> Sorry to dig up this old thread, but this is triggering false positives >> while make checking for people who don’t want to toy around with >> MACOSX_DEPLOYMENT_TARGET. >> Could/should we filter this somehow, or have BuildSystem tinker with the >> environment variable itself? >> >> Thanks, >> Pierre >> >> $ make check >> Running check examples to verify correct installation >> Using PETSC_DIR=/Users/jolivet/repo/petsc and >> PETSC_ARCH=arch-darwin-c-debug-real >> *******************Error detected during compile or link!******************* >> See http://www.mcs.anl.gov/petsc/documentation/faq.html >> <http://www.mcs.anl.gov/petsc/documentation/faq.html> >> /Users/jolivet/repo/petsc/src/snes/tutorials ex19 >> ********************************************************************************* >> mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined >> -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first >> -Wl,-no_compact_unwind -Wall -g -Wall -g >> -I/Users/jolivet/repo/petsc/include >> -I/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/include >> -I/opt/intel/mkl/include ex19.c >> -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib >> -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib >> -Wl,-rpath,/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib >> -L/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib >> -Wl,-rpath,/opt/intel/mkl/lib -L/opt/intel/mkl/lib -Wl,-rpath,/opt/intel/lib >> -L/opt/intel/lib -Wl,-rpath,/usr/local/Cellar/mpich/3.4.1_1/lib >> -L/usr/local/Cellar/mpich/3.4.1_1/lib >> -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 >> >> -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 >> -Wl,-rpath,/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 >> -L/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10 -lpetsc -lHYPRE -lcmumps >> -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmkl_scalapack_lp64 >> -lmkl_blacs_mpich_lp64 -lEl -lElSuiteSparse -lpmrrr -lp4est -lsc -liomp5 >> -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lparmmg -lmmg -lmmg3d >> -lptesmumps -lptscotchparmetis -lptscotch -lptscotcherr -lesmumps -lscotch >> -lscotcherr -lparmetis -lmetis -ltriangle -ltet -lz -lX11 -lc++ -ldl >> -lmpifort -lmpi -lpmpi -lgfortran -lquadmath -lm -lc++ -ldl -o ex19 >> ld: warning: dylib (/usr/local/Cellar/mpich/3.4.1_1/lib/libmpifort.dylib) >> was built for newer macOS version (11.1) than being linked (11.0) >> ld: warning: dylib >> (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgfortran.dylib) was built for >> newer macOS version (11.2) than being linked (11.0) >> ld: warning: dylib >> (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.dylib) was built for >> newer macOS version (11.2) than being linked (11.0) >> ld: warning: dylib >> (/usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libquadmath.0.dylib) was built >> for newer macOS version (11.2) than being linked (11.0) >> ld: warning: object file >> (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libcmumps.a(cana_aux.o)) >> was built for newer macOS version (11.2) than being linked (11.0) >> ld: warning: object file >> (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libdmumps.a(dana_aux.o)) >> was built for newer macOS version (11.2) than being linked (11.0) >> ld: warning: object file >> (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libsmumps.a(sana_aux.o)) >> was built for newer macOS version (11.2) than being linked (11.0) >> ld: warning: object file >> (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libzmumps.a(zana_aux.o)) >> was built for newer macOS version (11.2) than being linked (11.0) >> ld: warning: object file >> (/Users/jolivet/repo/petsc/arch-darwin-c-debug-real/lib/libmumps_common.a(front_data_mgt_m.o)) >> was built for newer macOS version (11.2) than being linked (11.0) >> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process >> >> >>> On 15 Feb 2021, at 6:08 PM, Jacob Faibussowitsch <jacob....@gmail.com >>> <mailto:jacob....@gmail.com>> wrote: >>> >>> Yes, this also seems to work on my end. >>> >>> Best regards, >>> >>> Jacob Faibussowitsch >>> (Jacob Fai - booss - oh - vitch) >>> Cell: (312) 694-3391 >>> >>>> On Feb 15, 2021, at 12:05, Satish Balay <ba...@mcs.anl.gov >>>> <mailto:ba...@mcs.anl.gov>> wrote: >>>> >>>> Does setting MACOSX_DEPLOYMENT_TARGET also work? >>>> >>>> Satish >>>> >>>> On Mon, 15 Feb 2021, Jacob Faibussowitsch wrote: >>>> >>>>> I think this problem ultimately stems from the fact that gcc/g++ and >>>>> gfortran are not from the same people on macOS. It seems like clang is >>>>> configured to build for 11.0 target, whilst gcc defaults to newest >>>>> available target. And indeed if I change my compile command there is no >>>>> warning: >>>>> >>>>> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && >>>>> gcc-10 -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib >>>>> -undefined dynamic_lookup && rm -rf ./build >>>>> >>>>> Note I now call gcc-10 as the linker which is the __actual__ gcc (not >>>>> clang in a trench coat). >>>>> >>>>> Best regards, >>>>> >>>>> Jacob Faibussowitsch >>>>> (Jacob Fai - booss - oh - vitch) >>>>> Cell: (312) 694-3391 >>>>> >>>>>> On Feb 15, 2021, at 11:46, Jacob Faibussowitsch <jacob....@gmail.com >>>>>> <mailto:jacob....@gmail.com>> wrote: >>>>>> >>>>>> Ok so if I pass -mmacosx-version-min=11.2 to the linker the warning >>>>>> disappears... >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Jacob Faibussowitsch >>>>>> (Jacob Fai - booss - oh - vitch) >>>>>> Cell: (312) 694-3391 >>>>>> >>>>>>> On Feb 15, 2021, at 11:41, Jacob Faibussowitsch <jacob....@gmail.com >>>>>>> <mailto:jacob....@gmail.com> <mailto:jacob....@gmail.com >>>>>>> <mailto:jacob....@gmail.com>>> wrote: >>>>>>> >>>>>>> I can reproduce the warning compiling just that simple code you listed. >>>>>>> This is the compile command: >>>>>>> >>>>>>> mkdir -p build && gfortran -c -o ./build/conftest.o conftest.F90 && gcc >>>>>>> -o ./build/libconftest.dylib ./build/conftest.o -dynamiclib -undefined >>>>>>> dynamic_lookup && rm -rf ./build >>>>>>> >>>>>>> And error: >>>>>>> ld: warning: object file (./build/conftest.o) was built for newer macOS >>>>>>> version (11.2) than being linked (11.0) >>>>>>> >>>>>>> Note I recently uninstalled and reinstalled command line tools too, >>>>>>> which does not seem to have fixed it. >>>>>>> >>>>>>> Best regards, >>>>>>> >>>>>>> Jacob Faibussowitsch >>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>> Cell: (312) 694-3391 >>>>>>> >>>>>>>> On Feb 15, 2021, at 11:30, Satish Balay <ba...@mcs.anl.gov >>>>>>>> <mailto:ba...@mcs.anl.gov> <mailto:ba...@mcs.anl.gov >>>>>>>> <mailto:ba...@mcs.anl.gov>>> wrote: >>>>>>>> >>>>>>>> Here is the compile command and the warning: >>>>>>>> >>>>>>>>>>>>>> >>>>>>>> ===== Checking linker >>>>>>>> Executing: gfortran -c -o >>>>>>>> /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o >>>>>>>> >>>>>>>> -I/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers >>>>>>>> >>>>>>>> /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.F90 >>>>>>>> >>>>>>>> Successful compile: >>>>>>>> Source: >>>>>>>> function foo(a) >>>>>>>> real:: a,x,bar >>>>>>>> common /xx/ x >>>>>>>> x=a >>>>>>>> foo = bar(x) >>>>>>>> end >>>>>>>> Executing: gcc -o >>>>>>>> /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/libconftest.dylib >>>>>>>> -dynamiclib -single_module -undefined dynamic_lookup >>>>>>>> -multiply_defined suppress >>>>>>>> /var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o >>>>>>>> >>>>>>>> Possible ERROR while running linker: >>>>>>>> stderr: >>>>>>>> ld: warning: object file >>>>>>>> (/var/folders/9w/7dlszmmn6q1gd5yf3r9n79bc0000gn/T/petsc-dk9aiv7x/config.setCompilers/conftest.o) >>>>>>>> was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>> Accepted FC PIC code without compiler flag >>>>>>>> >>>>>>>> ============================================================================================= >>>>>>>> <<<<<< >>>>>>>> >>>>>>>> Its likely due to the way brew built gfortran. You can try compiling a >>>>>>>> simple test code and see if you can reproduce this warning. >>>>>>>> >>>>>>>> There is a related issue at: >>>>>>>> >>>>>>>> https://github.com/spack/spack/issues/21644 >>>>>>>> <https://github.com/spack/spack/issues/21644> >>>>>>>> <https://github.com/spack/spack/issues/21644 >>>>>>>> <https://github.com/spack/spack/issues/21644>> >>>>>>>> >>>>>>>> Satish >>>>>>>> >>>>>>>> >>>>>>>> On Sat, 13 Feb 2021, Jacob Faibussowitsch wrote: >>>>>>>> >>>>>>>>> Hello All, >>>>>>>>> >>>>>>>>> I’ve been getting these warnings for weeks, at first I figured it was >>>>>>>>> due to gfortran brew package not being updated for Big Sur, but since >>>>>>>>> it has persisted through a few gfortran brew updates I’m thinking it >>>>>>>>> may be petsc related. This is on clean build on master. >>>>>>>>> >>>>>>>>> ld: warning: object file >>>>>>>>> (master-arch-darwin-c-debug/obj/sys/classes/bag/f2003-src/fsrc/bagenum.o) >>>>>>>>> was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>> ld: warning: object file >>>>>>>>> (master-arch-darwin-c-debug/obj/sys/f90-src/fsrc/f90_fwrap.o) was >>>>>>>>> built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>> ld: warning: object file >>>>>>>>> (master-arch-darwin-c-debug/obj/sys/objects/f2003-src/fsrc/optionenum.o) >>>>>>>>> was built for newer macOS version (11.2) than being linked (11.0) >>>>>>>>> ld: warning: object file >>>>>>>>> (master-arch-darwin-c-debug/obj/sys/fsrc/somefort.o) was built for >>>>>>>>> newer macOS version (11.2) than being linked (11.0) >>>>>>>>> ld: warning: object file >>>>>>>>> (master-arch-darwin-c-debug/obj/sys/f90-mod/petscsysmod.o) was built >>>>>>>>> for newer macOS version (11.2) than being linked (11.0) >>>>>>>>> >>>>>>>>> Best regards, >>>>>>>>> >>>>>>>>> Jacob Faibussowitsch >>>>>>>>> (Jacob Fai - booss - oh - vitch) >>>>>>>>> Cell: (312) 694-3391 >>> >> >